"Gnome 3 has received a lot of disapproval of late, from the Gnome foundation being charged with not taking care of its users, or losing mindshare, to Gnome 3 itself being an unusable mess. I've been using Gnome 3 myself for a few months to sort the truth from the fiction, and to try and understand just how the Gnome foundation expects their newest shell to be used. I will end with some thoughts on how Gnome 3 can be improved. The review will require a fairly lengthy preface, however."

It was about implicit behavior which is definitely not a desired pattern.
The hotspots are by nature invisible: that is fundamental bad design. An application, even a desktop, should expose its behavior, make it explicit and consistent. A desktop interface is widget driven, you input text in text areas, click on buttons, drag icons around: it's visible, it's clickable, it's interactive. I expect something to happen when I interact with a visible widget. Even if my hands are not incredibly agile I can move the cursor around and then stop and click. First, choose the target interactive widget, then willfully click or type to achieve interaction. I choose, then validate and trigger something. An invisible hotspot is absolutely not consistent with these concepts: I move the cursor to a zone, then an unvalidated intrusive event happens. It's not a flyover tooltip, it's my entire screen content that gets replaced with another, unrelated context.

They could have at least used a workaround, like the "show desktop zone" of Windows 7 (bottom right) which is explicit.

Consistency is why Macs have only one button. The right button is the "mystery contextual menu"; you can hardly guess what the menu contains in an application. Of course, two or three or even more buttons (and keyboard shortcuts) are better for advanced users, but the point is that it leads to confusing, inconsistent and unexpected behaviors.